Study finds significant inconsistencies in microbiome research methods
A research led by the UK’s Medicines and Healthcare products Regulatory Authority (MHRA) has found significant inconsistencies, at times false and incorrect results, in microbiome research methods used across the world
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A research led by the UK’s Medicines and Healthcare products Regulatory Authority (MHRA) has found significant inconsistencies, at times false and incorrect results, in microbiome research methods used across the world.
The study involved leading laboratories across multiple countries testing identical samples of gut microbiome bacteria.
Results revealed startling inconsistencies, with accuracy measures varying dramatically between laboratories – despite analysing the same samples highlighting an urgent need to adopt unified standards for the global harmonisation of gut microbiome research.
Key Findings
The researchers sent 23 laboratories in 11 countries across 4 continents and asked them to use the newly developed World Health Organization (WHO) International Reference Reagents – containing DNA of known bacterial compositions – to determine whether the methodologies were suitable.
When these laboratories analysed these samples, the results were shocking, the research published by American Society for Microbiology (ASM) said. The variations are in the lab results are:
- Species identification varied from 63% to 100% accuracy across different methods, meaning that some laboratories failed to detect a third of the bacterial species present in the sample
- False positive rates ranged from 0% to 41%, meaning some labs incorrectly identified bacteria that weren’t present in the sample
- Sample diversity estimates varied considerably, with labs identifying as few as 12 or as many as 185 different bacterial species in the same sample
Why this matters
The findings are important as microbiome research increasingly informs treatments for conditions including inflammatory bowel disease, metabolic syndrome, irritable bowel syndrome and colorectal cancer. However, contradictory findings between studies have undermined confidence in this rapidly expanding field.
The study identified that a key source of variation may arise from the application of “high throughput sequencing” methods applied to characterise gut microbiome samples. These variations arise from multiple steps in this method including:
Choice of DNA Sequencing Technology
- Bioinformatics software and databases used for analysis
- Version of reference databases (even minor updates significantly affected results)
- Laboratory protocols and techniques
The research further demonstrated that appropriate analysis methods could achieve accurate results with far fewer resources than previously thought (depending on the sample) – one laboratory achieved quality standards using approximately 890,000 DNA sequence reads, compared with others using an average of 25.4 million reads.
Minimum Quality Criteria
The study establishes Minimum Quality Criteria for four key reporting measures that laboratories worldwide can now use to validate their microbiome analysis methods. These standards are based on real-world data rather than theoretical predictions.
The WHO International DNA Gut Reference Reagents are now available for laboratories globally to benchmark their performance and optimise their methodologies.
Quality Standards for Patients
This UK government-funded research has created physical quality standards that laboratories worldwide can now use to assess the accuracy of their own detection methods. This means:
- Future gut health research will be more reliable
- Medical treatments based on microbiome science will be more trustworthy
- Your test results should become more reliable than before
- Progress towards new therapies for gut-related diseases should accelerate
The research - commissioned and funded by the Department of Health and Social Care Policy Research Programme through the MHRA Regulatory Science Research Unit, with additional support from an Innovate UK Small Business Research Initiative Award for “Creating Standards for Microbiome Therapies”, is helping to ensure that when doctors or researchers analyse your gut health, they’re getting accurate information – which means better diagnosis and treatment for everyone.
“This benchmark study highlights the true level of variability in microbiome data across the world and across sectors, underscoring the critical need for the use of WHO International DNA Gut Reference Reagents to elevate the quality of data in microbiome research. By pinpointing the sources of bias in existing methodologies using reference reagents, we can accelerate innovation and method optimisation", Saba Anwar, lead author of the study and Senior Research and Development Scientist at the MHRA, said.
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